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Installing the connector breaks JRE library

When I installed the connector, my OpenJPA project didn't see classes from JRE 
System Library. I still had 

    <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

in .classpath, but it wasn't visible in Package Explorer and was shown as 
"org.eclipse.jdt.launching.JRE_CONTAINER" instead of "JRE System Library" in 
the Configure Build Path dialog.

Original issue reported on code.google.com by [email protected] on 18 Jun 2012 at 8:01

plugin causing "Remote System Explorer Operation" that lock up Eclipse

What steps will reproduce the problem?
Unsure, happens after having Eclipse open for a while and doing normal
edits.  Doesn't seem to matter what is being edited.  Doesn't have to be a JPA 
entity.

What is the expected output? What do you see instead?
The lower left status area will flash every few seconds, basically unreadable 
because it's very brief.  Open the Progress view and there will be several 
"Remote System Explorer Operation" 
entries, almost always followed by 
"JPA Java Change Event Handler (Waiting)"
or
"JPA Project Change Event Handler (Waiting)"
and Eclipse is essentially useless (can't do anything that has to wait for 
those to complete, like saving a change) until all of the items in progress 
complete.  This can take a minute or two and is quite frustrating when all you 
want to do is save a change.

What version of the product are you using? On what operating system?
most recent version of this plugin
on
Version: Kepler Release
Build id: 20130614-0229
on 
Windows 7 x64 with all the latest updates.

Please provide any additional information below.
I had first entered this under Eclipse bugs here (see the bottom few entries)
https://bugs.eclipse.org/bugs/show_bug.cgi?id=386171

Original issue reported on code.google.com by [email protected] on 9 Aug 2013 at 2:07

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